Using Covalent Labeling and Mass Spectrometry To Study Protein Binding Sites of Amyloid Inhibiting Molecules

Abstract

Amyloid aggregates are associated with several debilitating diseases, and there are numerous efforts to develop small molecule treatments against these diseases. One challenge associated with these efforts is determining protein binding site information for potential therapeutics because amyloid-forming proteins rapidly form oligomers and aggregates, making traditional protein structural analysis techniques challenging. Using β-2-microglobulin (β2m) as a model amyloid-forming protein along with two recently identified small molecule amyloid inhibitors (i.e., rifamycin SV and doxycycline), we demonstrate that covalent labeling and mass spectrometry (MS) can be used to map small-molecule binding sites for a rapidly aggregating protein. Specifically, three different covalent labeling reagents, namely diethylpyrocarbonate, 2,3-butanedione, and the reagent pair EDC/GEE, are used together to pinpoint the binding sites of rifamycin SV, doxycycline, and another molecule, suramin, which binds but does not inhibit Cu(II)-induced β2m amyloid formation. The labeling results reveal binding sites that are consistent with the known effects of these molecules on β2m amyloid formation and are in general agreement with molecular docking results. We expect that this combined covalent labeling approach will be applicable to other protein/small molecule systems that are difficult to study by traditional means.

Figure 1

ESI‐MS titration curve, indicating the binding affinity of suramin to Cu(II)‐β2m. The meaning of R/(R+1) and how this information is used to determine K_a is shown in the Supporting Information.

Figure 2

Labeling results with rifamycin SV. (a) Changes in covalent labeling modification percentages with rifamycin SV bound to the Cu(II)‐protein complex. Error bars represent a single standard deviation from three replicate measurement. Asterisks above the bars represent the residues that undergo a significant change in modification level at a 95% confidence interval as determined by a two‐sample unpaired Student's t‐test. The arrows at the top of the graph indicate the locations and directions of the seven β strands in β2m. (b) Ribbon structure of β2m, showing the seven β strands labeled A through G. (c) β2m surface structure illustrating the sites of significant changes in covalent labeling induced by rifamycin SV. Sites that increase in labeling are colored red, while sites that decrease in labeling are colored blue. (d) Protein‐ligand docking result.

Figure 3

Labeling results with doxycycline. (a) Changes in covalent labeling modification percentages with doxycycline bound to the Cu(II)‐protein complex . Error bars represent a single standard deviation from three replicate measurement. Asterisks above the bars represent the residues that undergo a significant change in modification level at a 95% confidence interval as determined by a two‐sample unpaired Student's t‐test. The arrows at the top of the graph indicate the locations and directions of the seven β strands in β2m. (b) β2m surface structure illustrating the sites of significant covalent labeling changes induced by doxycycline. Sites that increase in labeling are colored red, while sites that decrease in labeling are colored blue. (c) Protein‐ligand docking result.

Figure 4

Labeling results with suramin. (a) Changes in covalent labeling modification percentages with suramin bound to the Cu(II)‐protein complex. Error bars represent a single standard deviation from three replicate measurement. Asterisks above the bars represent the residues that undergo a significant change in modification level at a 95% confidence interval as determined by a two‐sample unpaired Student's t‐test. The arrows at the top of the graph indicate the locations and directions of the seven β strands in β2m. (b) β2m surface structure illustrating the sites of significant covalent labeling changes induced by suramin. Sites that increase in labeling are colored red, while sites that decrease in labeling are colored blue. (c) Proposed suramin binding site based on covalent labeling data.